> From the user's point of view one of the most serious disadvantages of > the current Jmol version is the strange internal mechanism for > protein secondary structure determination.
I agree completely. It is broken. > One example is the structure 1srb. No examples are necessary > RasMol/Chime give for all 10 models one helix in the middle of the > sequence. > On the contrary, Jmol yields > Model Sheets (S), Helices (H) > 1 2 S > 2 2S,1H > 3 0S,0H > 4 1S > 5 1S > 6 2S > 7 1S,1H > 8 1S > 9 2S > 10 2S > > You may want to contact G. Vriend at the CMBI in Nijmegen/The Netherlands. > He seems to take care of the DSSP program written by W. Kabsch and C. > Sander. > (http://swift.cmbi.ru.nl/gv/dssp/). I contacted Gert several years ago, explained Jmol, and asked for his assistance. He explained that he was only the 'keeper' of the code and that he was not authorized to approve the release of the code for use under an open source license. He said that I needed to get approval from Chris Sander. I subsequently exchanged some emails with Chris Sander. In the end, I was unable to get approval for them to release the source code to me so that I could reimplement it in Java for use in Jmol under the GNU LGPL. After that experience I spent quite some time sending emails to authors of other programs for automatic identification of protein secondary structure. Several replied to my emails ... and I was optimistic that someone would help me out. Unfortunately, none of them followed through on their respones. I then spent several weeks reading research papers, but was unable to understand enough of the algorithms to build a decent implementation. My current position is as follows: Some else needs to lead the effort to get automatic identification of protein secondary structures built into Jmol. I believe that this needs to be someone who understands the problem and has implementation experience. I will certainly support the effort in any way that I can, but I will not lead the effort. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: Power Architecture Resource Center: Free content, downloads, discussions, and more. http://solutions.newsforge.com/ibmarch.tmpl _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
